tbuckley/cabot-search huggingface dataset:
Consistency regularisation in varying contexts and feature perturbations for semi-supervised semantic segmentation of histology images
Authors: Raja Muhammad Saad Bashir, Talha Qaiser, Shan E Ahmed Raza, Nasir M. Rajpoot
Journal: Medical Image Analysis (2023)

Semantic segmentation of various tissue and nuclei types in histology images is fundamental to many downstream tasks in the area of computational pathology (CPath). In recent years, Deep Learning (DL) methods have been shown to perform well on segmentation tasks but DL methods generally require a large amount of pixel-wise annotated data. Pixel-wise annotation sometimes requires expert's knowledge and time which is laborious and costly to obtain. In this paper, we present a consistency based semi-supervised learning (SSL) approach that can help mitigate this challenge by exploiting a large amount of unlabelled data for model training thus alleviating the need for a large annotated dataset. However, SSL models might also be susceptible to changing context and features perturbations exhibiting poor generalisation due to the limited training data. We propose an SSL method that learns robust features from both labelled and unlabelled images by enforcing consistency against varying contexts and feature perturbations. The proposed method incorporates context-aware consistency by contrasting pairs of overlapping images in a pixel-wise manner from changing contexts resulting in robust and context invariant features. We show that cross-consistency training makes the encoder features invariant to different perturbations and improves the prediction confidence. Finally, entropy minimisation is employed to further boost the confidence of the final prediction maps from unlabelled data. We conduct an extensive set of experiments on two publicly available large datasets (BCSS and MoNuSeg) and show superior performance compared to the state-of-the-art methods.
Local Delivery of Glabridin by Biomolecular Microneedle to Accelerate Infected Wound Healing
Authors: Zesheng Chen, Tao Hu, Rui Wang, Bohan Huang, Lingfeng Tu, Guanyi Wang, Cao Li, Binghai Dong, Zijian Wang, Weikang Hu
Journal: Advanced Healthcare Materials (2023)

Abstract Applying antibacterial polymers and pro‐regenerative small molecules are two individual strategies for accelerating wound healing. However, integrating those two unique approaches into one therapeutic platform that meets clinical requirements is still a challenge. Herein, a series of antibacterial gelatin methacrylate (GelMA)/ε‐polylysine (ε‐PL) composite hydrogels (termed as GP‐n HGs, n = 0, 10, 20, and 30, respectively) are innovatively fabricated by ultraviolet light (UV) crosslinking. The GP‐n HGs are proved to be broad‐spectrum antibacterial and biocompatible. Among those GP‐n HGs, the GP‐20 HG is selectively processed into microneedle following a mold‐casting method. Then, the glabridin is loaded into those needles to produce composite microneedle termed GP‐20@Gla MN. An S. aureus ‐infected full‐thickness defect model in rats is created to evaluate the wound‐healing effect of GP‐20@Gla MN. Furthermore, an RNA sequencing assay is performed to explore the possible molecular mechanisms of glabridin in promoting tissue regeneration, and many positive routes are summarized. This work is of significant novelty in fulfilling complex clinical needs by simultaneously optimizing the advanced microneedles' chemical compositions and physical structures. This work will provide a promising therapeutic platform for treating infected and chronic wounds.
Re: Elie Kaplan-Marans, Tenny R. Zhang, Jim C. Hu. Differing Recommendations on Prostate Biopsy Approach to Minimize Infections: An Examination of the European Association of Urology and American Urological Association Guidelines. Eur Urol. 2023;84:445–46
Authors: Fabian Falkenbach, Francesco Sanguedolce, Lars Budäus
Journal: European Urology (2023)
Chronic pain, cannabis legalisation, and cannabis use disorder among patients in the US Veterans Health Administration system, 2005 to 2019: a repeated, cross-sectional study
Authors: Deborah S Hasin, Melanie M Wall, Daniel M Alschuler, Zachary L Mannes, Carol Malte, Mark Olfson, Katherine M Keyes, Jaimie L Gradus, Magdalena Cerdá, Charles C Maynard, Salomeh Keyhani, Silvia S Martins, David S Fink, Ofir Livne, Yoanna McDowell, Scott Sherman, Andrew J Saxon
Journal: The Lancet Psychiatry (2023)
Re: Laura Bukavina, Amy N. Luckenbaugh, Michael S. Hofman, et al. Incorporating Prostate-specific Membrane Antigen Positron Emission Tomography in Management Decisions for Men with Newly Diagnosed or Biochemically Recurrent Prostate Cancer. Eur Urol 2022;83:521–33
Authors: Giorgio Gandaglia, Francesco Barletta, Alberto Briganti, Francesco Montorsi
Journal: European Urology (2023)
Reply to Qingpeng Xie and Dianqiu Shen’s Letter to the Editor re: Bhavan P. Rai, José Luis Dominguez Escrig, Luís Vale, et al. Systematic Review of the Incidence of and Risk Factors for Urothelial Cancers and Renal Cell Carcinoma Among Patients with Haematuria. Eur Urol 2022;82:182–92
Authors: Bhavan Prasad Rai, Philippe D. Violette, Muhammad Imran Omar
Journal: European Urology (2023)
Mechanoresponse of Curved Epithelial Monolayers Lining Bowl‐Shaped 3D Microwells
Authors: Marine Luciano, Marie Versaevel, Yohalie Kalukula, Sylvain Gabriele
Journal: Advanced Healthcare Materials (2023)

Abstract The optimal functioning of many organs relies on the curved architecture of their epithelial tissues. However, the mechanoresponse of epithelia to changes in curvature remains misunderstood. Here, bowl‐shaped microwells in hydrogels are designed via photopolymerization to faithfully replicate the shape and dimensions of lobular structures. Leveraging these hydrogel‐based microwells, curved epithelial monolayers are engineered, and how in‐plane and Gaussian curvatures at the microwell entrance influence epithelial behavior is investigated. Cells and nuclei around the microwell edge display a more pronounced centripetal orientation as the in‐plane curvature decreases, and enhanced cell straightness and speed. Moreover, cells reorganize their actin cytoskeleton by forming a supracellular actin cable at the microwell edge, with its size becoming more pronounced as the in‐plane curvature decreases. The Gaussian curvature at the microwell entrance enhances the maturation of the supracellular actin cable architecture and leads to a vertical orientation of nuclei toward the bottom of the microwell. Increasing Gaussian curvature results in flattened and elongated nuclear morphologies characterized by highly compacted chromatin states. This approach provides better understanding of the mechanoresponse of curved epithelial monolayers curvatures lining lobular structures. In addition, bowl‐shaped microwells offer a powerful platform to study curvature‐dependent mechanotransduction pathways in anatomically relevant 3D structures.
SurgT challenge: Benchmark of soft-tissue trackers for robotic surgery
Authors: João Cartucho, Alistair Weld, Samyakh Tukra, Haozheng Xu, Hiroki Matsuzaki, Taiyo Ishikawa, Minjun Kwon, Yong Eun Jang, Kwang-Ju Kim, Gwang Lee, Bizhe Bai, Lueder A. Kahrs, Lars Boecking, Simeon Allmendinger, Leopold Müller, Yitong Zhang, Yueming Jin, Sophia Bano, Francisco Vasconcelos, Wolfgang Reiter, Jonas Hajek, Bruno Silva, Estevão Lima, João L. Vilaça, Sandro Queirós, Stamatia Giannarou
Journal: Medical Image Analysis (2023)
The immune response to SARS-CoV-2 in people with HIV
Authors: Maxine A. Höft, Wendy A. Burgers, Catherine Riou
Journal: Cellular and Molecular Immunology (2023)

Abstract This review examines the intersection of the HIV and SARS-CoV-2 pandemics. People with HIV (PWH) are a heterogeneous group that differ in their degree of immune suppression, immune reconstitution, and viral control. While COVID-19 in those with well-controlled HIV infection poses no greater risk than that for HIV-uninfected individuals, people with advanced HIV disease are more vulnerable to poor COVID-19 outcomes. COVID-19 vaccines are effective and well tolerated in the majority of PWH, though reduced vaccine efficacy, breakthrough infections and faster waning of vaccine effectiveness have been demonstrated in PWH. This is likely a result of suboptimal humoral and cellular immune responses after vaccination. People with advanced HIV may also experience prolonged infection that may give rise to new epidemiologically significant variants, but initiation or resumption of antiretroviral therapy (ART) can effectively clear persistent infection. COVID-19 vaccine guidelines reflect these increased risks and recommend prioritization for vaccination and additional booster doses for PWH who are moderately to severely immunocompromised. We recommend continued research and monitoring of PWH with SARS-CoV-2 infection, especially in areas with a high HIV burden.
At the Head and Heart of Oxytocin’s Stress-Regulatory Neural and Cardiac Effects: A Chronic Administration RCT in Children with Autism
Authors: Kaat Alaerts, Nicky Daniels, Matthijs Moerkerke, Margaux Evenepoel, Tiffany Tang, Stephanie Van der Donck, Viktoria Chubar, Stephan Claes, Jean Steyaert, Bart Boets, Jellina Prinsen
Journal: Psychotherapy and Psychosomatics (2023)

Introduction: Intranasal administration of oxytocin presents a promising new approach to reduce disability associated with an autism spectrum disorder diagnosis. Previous investigations have emphasized the amygdala as the neural foundation for oxytocin’s acute effects. However, to fully understand oxytocin’s therapeutic potential, it is crucial to gain insight into the neuroplastic changes in amygdala circuitry induced from chronic oxytocin administrations, particularly in pediatric populations. Objective: We aimed to examine the impact of a 4-week course of intranasal oxytocin on amygdala functional connectivity in children with autism, compared to placebo. Additionally, we investigated whether oxytocin improves cardiac autonomic arousal, as indexed by high-frequency heart rate variability. Methods: Fifty-seven children with autism aged 8–12 years (45 boys, 12 girls) participated in a double-blind, randomized pharmaco-neuroimaging trial involving twice-daily administrations of intranasal oxytocin or placebo. Resting-state fMRI scans and simultaneous, in-scanner heart rate recordings were obtained before, immediately after, and 4 weeks after the nasal spray administration period. Results: Significant reductions in intrinsic amygdala-orbitofrontal connectivity were observed, particularly at the 4-week follow-up session. These reductions were correlated with improved social symptoms and lower cardiac autonomic arousal. Further, oxytocin’s neural and cardiac autonomic effects were modulated by epigenetic modifications of the oxytocin receptor gene. The effects were more pronounced in children with reduced epigenetic methylation, signifying heightened expression of the oxytocin receptor. Conclusion: These findings underscore that a 4-week oxytocin administration course decreases amygdala connectivity and improves cardiac autonomic balance. Epigenetic modulators may explain inter-individual variation in responses to oxytocin.
Survival Outcome Analysis of Stereotactic Body Radiotherapy and Immunotherapy (SBRT-IO) versus SBRT-Alone in Unresectable Hepatocellular Carcinoma
Authors: Chi Leung Chiang, Francis Ann Shing Lee, Kenneth Sik Kwan Chan, Venus Wan Yan Lee, Keith Wan Hang Chiu, Ryan Lok Man Ho, John Ka Shun Fong, Natalie Sean Man Wong, Winnie Wing Ling Yip, Cynthia Sin Yu Yeung, Vince Wing Hang Lau, Kwan Man, Feng Ming Spring Kong, Albert Chi Yan Chan
Journal: Liver Cancer (2023)

&lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; While combination of stereotactic body radiotherapy (SBRT) and immunotherapy are promising, their efficacy and safety have not been compared with SBRT-alone in patients with unresectable hepatocellular carcinoma (HCC). &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; This retrospective study included 100 patients with nonmetastatic, unresectable HCC in two hospitals. Eligible patients had tumor nodules ≤3 and Child-Pugh liver function score of A5 to B7. Seventy patients received SBRT-alone, and 30 patients underwent combined SBRT and immunotherapy (SBRT-IO). Overall survival (OS), time to progression (TTP), overall response rate (ORR), and toxicity were analyzed. We adjusted for the potential confounding factors using propensity score matching. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; The median tumor size was 7.3 cm (range, 2.6–18 cm). Twenty-five (25%) of patients had vascular invasion. Before propensity score matching, the 1-year and 3-year OS rate was 89.9% and 59.8% in the SBRT-IO group and 75.7% and 42.3% in SBRT-alone group (&lt;i&gt;p&lt;/i&gt; = 0.039). After propensity score matching (1:2), 25 and 50 patients were selected from the SBRT-IO and SBRT-alone group. The 1-year and 3-year OS was 92.0% and 63.9% in the SBRT-IO group versus 74.0% and 43.3% in the SBRT-alone group (&lt;i&gt;p&lt;/i&gt; = 0.034). The 1-year and 3-year TTP was better in SBRT-IO group (1-year: 68.9% vs. 58.9% and 3-year: 61.3% vs. 32.5%, &lt;i&gt;p&lt;/i&gt; = 0.057). The ORR of 88% (complete response [CR]: 56%, partial response [PR]: 22%) in SBRT-IO arm was significantly better than 50% (CR: 20%, PR: 30%) in the SBRT-alone arm (&lt;i&gt;p&lt;/i&gt; = 0.006). Three patients (12%) developed ≥grade 3 immune-related treatment adverse events (&lt;i&gt;n&lt;/i&gt; = 2 hepatitis, &lt;i&gt;n&lt;/i&gt; = 1 dermatitis) leading to permanent treatment discontinuation. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; Adding immunotherapy to SBRT resulted in better survival with manageable toxicities. Prospective randomized trial is warranted.
Genetic/Epigenetic Alteration and Tumor Immune Microenvironment in Intrahepatic Cholangiocarcinoma: Transforming the Immune Microenvironment with Molecular-Targeted Agents
Authors: Naoshi Nishida, Masatoshi Kudo
Journal: Liver Cancer (2023)

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Intrahepatic cholangiocarcinoma (iCCA) is often diagnosed at an advanced stage, leading to limited treatment options and a poor prognosis. So far, standard systemic therapy for advanced iCCA has been a combination of gemcitabine and cisplatin. However, recent advancements in the understanding of the molecular characteristics of iCCA have opened new possibilities for molecular-targeted therapies and immunotherapy. &lt;b&gt;&lt;i&gt;Summary:&lt;/i&gt;&lt;/b&gt; Reportedly, 9–36% of iCCA cases have an inflamed tumor immune microenvironment (TME) based on the immune gene expression signature, which is characterized by the presence of immune cells involved in anti-tumor immune responses. The majority of iCCA cases have a non-inflamed TME with a lack of effector T cells, rendering immune checkpoint inhibitors (ICIs) ineffective in these cases. Interestingly, alterations in the fibroblast growth factor receptor (&lt;i&gt;FGFR2&lt;/i&gt;) gene and &lt;i&gt;IDH1/2&lt;/i&gt; gene mutations are often observed in the non-inflamed TME in iCCA. Several mechanisms have been reported for the role of driver mutations on the establishment of TME unique for iCCA. For example, &lt;i&gt;IDH1/2&lt;/i&gt; mutations, which cause an increase in DNA methylation, are associated with the downregulation and hypermethylation of antigen processing and presentation machinery, which may contribute to the establishment of a non-inflamed TME. Therefore, inhibitors targeting &lt;i&gt;IDH1/2&lt;/i&gt; may restore the DNA methylation and expression status of molecules involved in antigen presentation, potentially improving the efficacy of ICIs. FGFR inhibitors may also have the potential to modulate immunosuppressive TME by inhibitingthe suppressor of cytokine signaling 1 and activating the interferon-γ signaling as a consequence of inhibition of the &lt;i&gt;FGFR&lt;/i&gt; signal. From this perspective, understanding the molecular characteristics of iCCA, including the TME and driver mutations, is essential for the effective application of ICIs and molecular-targeted therapies. &lt;b&gt;&lt;i&gt;Key Messages:&lt;/i&gt;&lt;/b&gt; Combination approaches that target both the tumor and immune system hold promise for improving the outcomes of patients with iCCA. Further research and clinical trials are needed to validate these approaches and optimize the treatment strategies for iCCA.
Real-World Data on the Diagnosis, Treatment, and Management of Hepatocellular Carcinoma in the Asia-Pacific: The INSIGHT Study
Authors: Yu Ki Sim, Ming Chuen Chong, Mihir Gandhi, Yogesh Mahadev Pokharkar, Yanan Zhu, Luming Shi, Li Lequn, Chien-Hung Chen, Masatoshi Kudo, Joon Hyeok Lee, Simone I Strasser, Rawisak Chanwat, Pierce K H Chow
Journal: Liver Cancer (2023)

&lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; Hepatocellular carcinoma (HCC) is the sixth most commonly diagnosed cancer and the third leading cause of cancer death worldwide. While there has been rapid evolution in the treatment paradigm of HCC across the past decade, the extent to which these newly approved therapies are utilized in clinical practice in the real world is, however, unknown. The INSIGHT study was an investigator-initiated, multi-site longitudinal cohort study conducted to reflect real-world epidemiology and clinical practice in Asia-Pacific in the immediate 7-year period after the conclusion of the BRIDGE study. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Data were collected both retrospectively (planned 30% of the total cohort size) and prospectively (planned 70%) from January 2013 to December 2019 from eligible patients newly diagnosed with HCC from 33 participating sites across 9 Asia-Pacific countries. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; A total of 2,533 newly diagnosed HCC patients (1,052 in retrospective cohort and 1,481 in prospective cohort) were enrolled. The most common risk factor was hepatitis B in all countries except Japan, Australia, and New Zealand, where the prevalence of hepatitis C and diabetes were more common. The top three comorbidities reported in the INSIGHT study include cirrhosis, hypertension, and diabetes. We observe high heterogeneity in the first-line treatment recorded across countries and across disease stages, which significantly affects survival outcomes. Stratification by factors such as etiologies, tumor characteristics, the presence of extrahepatic metastases or macrovascular invasion, and the use of subsequent lines of treatment were performed. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; The INSIGHT study describes a wide spectrum of clinical management practices in HCC, where patient demographics, differential costs, and patient access to therapies may lead to wide geographical variations through the patient’s treatment cycle, from diagnosis to clinical outcome. The high heterogeneity in patient outcomes demonstrates the need for more robust and clinical management strategies to be designed and adopted to bring about better patient outcomes.
Shiitake Dermatitis
Authors: Eglė Janušonytė, Jöri Pünchera
Journal: New England Journal of Medicine (2023)

A 72-year-old man presented to the emergency department with a 2-day history of an itchy rash on his back.The intensity of the itching had impaired his ability to sleep.Two days before the onset of the rash, he had prepared and eaten a meal containing shiitake mushrooms.On physical examination, edematous, flagellate plaques and linear patches were present across the patient's entire back and upper buttocks.There was no adenopathy, dermographism, or mucosal involvement.A diagnosis of shiitake dermatitis was made.Shiitake dermatitis occurs after consumption of raw or undercooked shiitake mushrooms.The characteristic streaky rash -also known as flagellate erythema -may also be seen after exposure to bleomycin or, in rare cases, in dermatomyositis or adult-onset Still's disease.A dietary history clinches the diagnosis.The patient was reassured about the self-limited nature of the condition and was advised to fully cook shiitake mushrooms in the future.Topical glucocorticoids and oral antihistamines were also given for treatment of the symptoms.At the 2-week followup, residual areas of postinflammatory hyperpigmentation were present, but the itchiness had abated.
Shiga Toxin–Producing <i>Escherichia coli</i> and the Hemolytic–Uremic Syndrome
Authors: Stephen B. Freedman, Nicole C.A.J. van de Kar, Phillip I. Tarr
Journal: New England Journal of Medicine (2023)

Shiga toxin–producing E. coli causes clinically important morbidity, particularly in children. Use of optimized diagnostics for identifying STEC and reporting toxin genotypes is essential.
Catheter Ablation for Atrial Fibrillation in Heart Failure — An Option to Defer Transplantation?
Authors: Eldrin F. Lewis
Journal: New England Journal of Medicine (2023)

Patients with heart failure often have coexisting atrial fibrillation, and the incidence of atrial fibrillation is higher among patients with more advanced heart failure (ranging from 5% among those with New York Heart Association [NYHA] class I disease to 50% among those with NYHA class IV disease).1 The coexistence of heart failure and atrial fibrillation is associated with an increased risk of hospitalization and death.1 Atrial fibrillation may lead to neurohormonal activation, cardiac remodeling, inflammation, and tachycardia-mediated worsening of left ventricular function, and progression of heart failure can increase the incidence and burden of atrial fibrillation. Evidence for catheter ablation . . .
Timing Is Everything — Evidence for When to Perform Complete Revascularization in STEMI
Authors: W. Schuyler Jones
Journal: New England Journal of Medicine (2023)

The performance of complete revascularization in patients with multivessel coronary artery disease and ST-segment elevation myocardial infarction (STEMI) has been a topic of debate. This scenario is extremely common, given that multivessel coronary artery disease is detected during index coronary angiography in approximately 50% of patients with STEMI.1 Although current guidelines from the American College of Cardiology and American Heart Association consider staged percutaneous coronary intervention (PCI) a class I indication for non–infarct-related artery stenosis,2 during the previous 10 years extreme uncertainty existed about whether any non–infarct-related lesions should be revascularized, including lesions present in patients with concomitant cardiogenic shock. . . .
Adjunctive Dexamethasone for Tuberculous Meningitis in HIV-Positive Adults
Authors: Joseph Donovan, Nguyen D. Bang, Darma Imran, Ho D.T. Nghia, Erlina Burhan, Dau T.T. Huong, Nguyen T.T. Hiep, Lam H.B. Ngoc, Dang V. Thanh, Nguyen T. Thanh, Anna L.S. Wardhani, Kartika Maharani, Cakra P. Gasmara, Nguyen H.H. Hanh, Pham K.N. Oanh, Riwanti Estiasari, Do D.A. Thu, Ardiana Kusumaningrum, Le T. Dung, Do C. Giang, Dang T.M. Ha, Nguyen H. Lan, Nguyen V.V. Chau, Nguyen T.M. Nguyet, Ronald B. Geskus, Nguyen T.T. Thuong, Evelyne Kestelyn, Raph L. Hamers, Nguyen H. Phu, Guy E. Thwaites
Journal: New England Journal of Medicine (2023)

Adjunctive glucocorticoids are widely used to treat human immunodeficiency virus (HIV)-associated tuberculous meningitis despite limited data supporting their safety and efficacy.
Empagliflozin improves cardiac energetics during ischaemia/reperfusion by directly increasing cardiac ketone utilization
Authors: Dylan Chase, Thomas R Eykyn, Michael J Shattock, Yu Jin Chung
Journal: Cardiovascular Research (2023)

Empagliflozin (EMPA), a potent inhibitor of the renal sodium-glucose cotransporter 2 and an effective treatment for Type 2 diabetes, has been shown to have cardioprotective effects, independent of improved glycaemic control. Several non-canonical mechanisms have been proposed to explain these cardiac effects, including increasing circulating ketone supply to the heart. This study aims to test whether EMPA directly alters cardiac ketone metabolism independent of supply.